Title: Letter to the editor in "Wrestling with SUMO and bio-ontologies"

Abstract

In this article, we analyze the current state of application of ontologies in biology, try to reveal the reasons for the existing difficulties, recommend a possible solution to the current problems and describe prospects and future challenges for the application of ontologival engineering in biological domains. We focus on the example of the ontology developed by the Microarray Gene Expression Society (MGED) for describing microarray experiments. We have chosen this example not because it is particularly bad, but because it exhibits the typical problems of biologival ontologies, and beause MGED has been promoted as an international standard. We wholeheartedly agree that such standards are extremely valuable, but we also believe that their promoters are particularly obliged to get them right, otherwise their whole advantage is negated.

@article{osti_909684,
title = {Letter to the editor in "Wrestling with SUMO and bio-ontologies"},
author = {Stoeckert, Christian Jr. J. and Ball, Cathy and Brazma, Alvis and Brinkman, Ryan and Causton, Helen C. and Fan, Liju and Fostel, Jennifer and Fragoso, Gilberto and Heiskanen, Mervi and Holstege, Frank and Morrison, Norman and Parkinson, Helen E. and Quackenbush, John and Rocca-Serra, Philippe and Sansone, Susanna A. and Sarkans, Ugis and Sherlock, Gavin and Stevens, Robert and Taylor, Chris and Taylor, Ronald C. and Whetzel, Patricia and White, Joseph C.},
abstractNote = {In this article, we analyze the current state of application of ontologies in biology, try to reveal the reasons for the existing difficulties, recommend a possible solution to the current problems and describe prospects and future challenges for the application of ontologival engineering in biological domains. We focus on the example of the ontology developed by the Microarray Gene Expression Society (MGED) for describing microarray experiments. We have chosen this example not because it is particularly bad, but because it exhibits the typical problems of biologival ontologies, and beause MGED has been promoted as an international standard. We wholeheartedly agree that such standards are extremely valuable, but we also believe that their promoters are particularly obliged to get them right, otherwise their whole advantage is negated.},
doi = {10.1038/nbt0106-21b},
journal = {Nature Biotechnology, 24(1):21-22},
number = 1,
volume = 24,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}

This letter to the editor of Journal of Radiological Protection is in response to a letter to the editor from G. M. Smith and M. C. Thorne of Great Britain concerning the appropriate selection of dose coefficients for ingested carbon-14 and chlorine-36, two of the most important long-lived components of radioactive wastes. Smith and Thorne argue that current biokinetic models of the International Commission on Radiological Protection (ICRP) for carbon and chlorine are overly cautious models from the standpoint of radiation dose estimates for C-14 and Cl-36, and that more realistic models are needed for evaluation of the hazards ofmore » these radionuclides in nuclear wastes. We (Harrison and Leggett) point out that new biokinetic models for these and other elements (developed at ORNL) will soon appear in ICRP Publications. These new models generally are considerably more realistic than current ICRP models. Here, examples are given for C-14 inhaled as carbon dioxide or ingested in water as bicarbonate, carbonate, or carbon dioxide.« less

It is not appropriate to use a thermodynamic function for an oxide that is not in equilibrium with its environment, as is the case for an oxide catalyst in an oxygen-free flow of nitrogen-cyclohexane. The volcano-shaped relationship between activity and heat of formation discussed by M. S. Wagh is therefore questionable. Graphs.